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targetHub API Documentation

targetHub is a database of miRNA-mRNA interactions. The interaction data is obtained various external data sources and in some cases computed in-house by algorithms implemented for miRNA target prediction.

The target prediction methods/data sources used to populate targetHub are shown in the following list. You can refer the documentation section for more details

Other sources may be incorporated in the future. These sources of information have been combined into a simple CouchDB database. As a consequence, we can build tools that make it possible to find the miRNA-gene interactions from various types of identifiers by different criteria using the CouchDB views.

Input and Output

All calls to read data or query results from the targetHub web service are made using RESTful HTTP calls. All results are returned in JavaScript Object Notation (JSON).targetHub follows the usual CouchDB conventions. Each object has a unique identifier, which in this case is given by pair of miRNA and a protein-coding gene seperated by a colon [depicting their interaction].

For example, the identifier of the document depicting the interaction of mir-212 with BRCA1 gene (Entrez Gene: 672) would be "hsa-mir-212:672". To get the JSON representation of this CouchDB document, send a HTTP GET request to the following URL:


HOSTNAME/tarhub/hsa-mir-212:672

Views

CouchDB queries are also known as views. The available views define the main API. In the current version, all views used to query the database are contained in the "basic" design document. You can get a copy of the design document by sending an HTTP GET request to the URL:


HOSTNAME/tarhub/_design/basic

Views are defined in targetHub to enable the user to query database by two different search options using three types of identifiers.

Search Options Three ways to query targetHub To use the API, each of the "HTTP calls" described in the following sections should be preceeded by


HOSTNAME/tarhub/_design/basic/_view/
Notes on Query-URL

Query by gene [Entrez Gene ID]

HTTP Call Search By Result
by_geneIDcount?key=["672",3] Evidence Count miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by exactly three data sources/methods
by_geneIDcount?startkey=["672",3]&endkey=["672",{}] Evidence Count miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by atleast three data sources/methods
by_geneIDmethod?key=["672","mirtarbase"] Specific Method miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by miRTarBase
by_geneIDmethod?key=["672","miranda+pictar4+targetscan"] Specific Method miRNA-target interactions of Entrez Gene "672" (BRCA1) that are supported by three methods miRanda, PicTar (4)and TargetScan

geneSmash: Web-service for gene ID conversion

geneSmash is a a gene-centric couchDB database containing information about human genes from various sources. The gene-based search interface for the targetHub website is built using geneSmash. The geneSmash web service converts any of the input gene identifier types to Entrez Gene. The Entrez Gene identifiers can then be passed on to query targetHub to retreive the relevant miRNA-target interactions. Similarly, when using the targetHub API you can utlize the geneSmash API to convert your gene identifier to Entrez Gene before querying targetHub [Sample Code in R]. Check geneSmash documentation for detailed information on web-service for gene ID conversion.

Query by stem-loop miRNA [mirbase ID]

HTTP Call Search By Result
by_miRNAIDcount?key=["hsa-mir-212",4] Evidence Count miRNA-target interactions of miRNA "hsa-mir-212" that are supported by exactly four data sources/methods
by_miRNAIDcount?startkey=["hsa-mir-212",3]&endkey=["hsa-mir-212",{}] Evidence Count miRNA-target interactions of miRNA "hsa-mir-212" that are supported by atleast three data sources/methods
by_miRNAIDmethod?key=["hsa-mir-212","pictar5"] Specific Method miRNA-target interactions of miRNA "hsa-mir-212" that are supported by PicTar (5)
by_miRNAIDmethod?key=["hsa-mir-212","miranda+mirtarbase+pictar4+targetscan"] Specific Method miRNA-target interactions of miRNA "hsa-mir-212" that are supported by four methods miRanda, miRTarBase, PicTar (4)and TargetScan

Query by mature miRNA [mirbase]

HTTP Call Search By Result
by_matureMIRcount?key=["hsa-miR-212-3p",4] Evidence Count miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by exactly four data sources/methods
by_matureMIRcount?startkey=["hsa-miR-212-3p",4]&endkey=["hsa-miR-212-3p",{}] Evidence Count miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by atleast four data sources/methods
by_matureMIRmethod?key=["hsa-miR-212-3p","targetscan"] Specific Method miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by TargetScan
by_matureMIRmethod?key=["hsa-miR-212-3p","miranda+targetscan"] Specific Method miRNA-target interactions of mature miRNA "hsa-miR-212-3p" (stem-loop: hsa-mir-212) that are supported by two methods miRanda and TargetScan